5-158588895-G-A

Variant names:

• chr5-158588895-G-A
• rs1122080
• ENST00000720334.1:n.517G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000720334.1(ENSG00000254135):​n.517G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,154 control chromosomes in the GnomAD database, including 3,670 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (3670 hom., cov: 32)
• Consequence: ENSG00000254135 ENST00000720334.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.29
• Publications: 8 publications found

Genes affected

ENSG00000254135 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254135	ENST00000720334.1	n.517G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32164 AN: 152036 Hom.: 3663 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.216

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.212 AC: 32194 AN: 152154 Hom.: 3670 Cov.: 32 AF XY: 0.211 AC XY: 15711 AN XY: 74378

African (AFR) AF: 0.241 AC: 9991 AN: 41492

American (AMR) AF: 0.255 AC: 3893 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 531 AN: 3468

East Asian (EAS) AF: 0.304 AC: 1574 AN: 5178

South Asian (SAS) AF: 0.367 AC: 1764 AN: 4812

European-Finnish (FIN) AF: 0.105 AC: 1109 AN: 10598

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12664 AN: 68006

Other (OTH) AF: 0.216 AC: 457 AN: 2112

Alfa AF: 0.190 Hom.: 355

Bravo AF: 0.222

Asia WGS AF: 0.341 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	18
DANN	Benign	0.73
PhyloP100		3.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1122080; hg19: chr5-158015903;